AMBER Archive (2000)

Subject: protein capping

From: Francois Dupradeau (fyd_at_u-picardie.fr)
Date: Fri Mar 17 2000 - 18:35:29 CST

Dear All,

I have a very simple question :

Is it possible to minimize (for instance) a peptide with a NH2_terminal
groupe and a COOH_terminal groupe with the amber94...98 force fields
instead of the NH3+_terminal and COO-_terminal groupes with amber_5 or 6
?

If I look in the amino acid database (all_amino94.in, all_aminoct94.in,
all_aminont94.in), I see ONLY 2 types of amino acids (AA):
NH3+_AA (N-term) and NH_AA (peptide bond) but I do not see the NH2_AA
(N-term) one.
COO-_AA (C-term) and CO_AA (peptide bond) but I do not see the COOH_AA
(C-term) one.

Thanks
Francois 

-- 
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  F.-Y. Dupradeau
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Faculte de Pharmacie, 1 rue des Louvels, F-80037 Amiens cedex 1, France
Tel 33 (0)322827494, Fax 33 (0)322827469, Email fyd_at_u-picardie.fr